Spatial Transcriptomic Profiling of Neurons in Mouse Striatum

  • 7:30 am (PDT)


NanoString has started an ambitious project called the “Spatial Organ Atlas.” The goal of this initiative is to map the architecture of tissues with spatially resolved whole transcriptomics. In this study, we used the GeoMx® Mouse Whole Transcriptome Atlas (WTA) to segment and profile different structures of the mouse brain at the cellular and molecular level. Spatial whole transcriptomic data was benchmarked to orthogonal platforms as an independent validation of the results.

In a follow-up study done in conjunction with our collaborators at Emory University in Ellen Hess’ lab, we performed deep spatial transcriptomic profiling using GeoMx Mouse WTA on subpopulations of spiny projection neurons (SPNs) in the mouse striatum. SPN subpopulations are generally divided into those that express D1 dopamine receptors and those that express D2 dopamine receptors. Recently, it was shown that these subpopulations are more complex than previously thought whereby gene expression in SPNs is, in part, mediated by their position within regional striatal subdivisions.

To analyze SPNs, 10um fresh frozen coronal sections from six C57/BL6 (WT) mice (n=3 female, n=3 male) were placed across two slides. D1 and D2 SPNs were identified using Drd1 and Adora2a RNAScope probes respectively in combination with Syto13 for visualization of all nuclei. Regions of interest (ROIs) were selected in dorsomedial, dorsolateral, and ventrolateral striatum to identify cell-type specific gene expression signatures in regions previously associated with unique functional roles within the striatum. GeoMx data was benchmarked against bulk and single-cell RNAseq from matched samples with high concordance across all metrics, and spatial analysis yielded novel insights into striatal organization of SPNs in WT mice. 

Alison VanSchoiack, PhD

Senior Product Enablement Scientist,

NanoString Technologies

Speaker Bio

Alison VanSchoiack is a Senior Product Enablement Scientist at NanoString Technologies and has a background in neurogenetics and neurodevelopmental disorders. Alison manages the Customer Experience Lab at NanoString’s Seattle headquarters and has worked extensively with external collaborators and customers to facilitate applied research with the GeoMx Digital Spatial Profiler (DSP). She earned her BA in Psychobiology from Occidental College and her PhD in Neuroscience from Arizona State University, and completed postdoctoral training at Seattle Children’s Research Institute.

FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.